In many regions species are declining due to fragmentation and loss of habitat. If species persistence isto be achieved, ecologically informed, effective conservation action is required. Yet it remains a challenge to identify optimal places in a landscape to direct habitat reconstruction and management. Rather than relying on individual landscape metrics, process-based regional scale assessment methodology is needed that focuses primarily on species persistence. This means integrating, according to species' ecology, habitat extent, suitability, quality and spatial configuration. The rapid evaluation of metapopulation persistence (REMP) methodology has been developed for this purpose. However, till now no practical conservation planning application of REMP has been described. By integration of expert ecological knowledge, we extended REMP's capabilities to prioritize conservation action for a highly modified agricultural region of central NSW, Australia based on the metapopulation ecology of 34 fauna species. The region's current capacity to support the species was evaluated in relation to the pre-European state for which there was known viability. Six of the species were found to currently have insufficient habitat to support viable populations. Seeking locations to maximize overall improvement in viability for these species, we prioritized conservation action to locations near the threshold of metapopulation persistence.